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Rare superfloods may cause rivers to change course, scientists say, compromising a site the Australian government has shortlisted for a nuclear waste dump.

Hydrogeologist, Peter Jolly of the Northern Territory's environment department, who previously raised concerns about the suitability of the proposed dump site at Fishers Ridge, now also casts doubt on the Harts Range site, 100 kilometres northeast of Alice Springs.

Jolly says the Harts Range site is on a flood plain between two active river channels that come off the ranges.

He says evidence shows that over hundreds or thousands of years massive flooding has been responsible for "catastrophic changes" in the course of rivers in Central Australia.

"A river goes in one spot at the moment but a megaflood can lead to it changing its course completely," says Jolly.

He says such issues are important to consider given the long-term nature of a nuclear dump.

"The river channels may migrate across the [dump] site, so if you're looking at a containment time of 500 years or a couple of hundred years, the site may end up in the river channel at some stage."

Jolly also says recent studies of water bores drilled near the two sites show there is an aquifer in river sediments of sand and gravel beneath the Harts Ranges site.

"That would tend to suggest that anything that would leak would leak pretty quickly into the sand and gravel and into the groundwater," he says.

But he says the other site at Mount Everard, 27 kilometres northwest of Alice Springs, has more suitable hydrogeology (water flow) and geomorphology (river erosion of the landscape) for a dump.

This site has brackish saline water beneath it, as well as 50 to 90 metres of clay, then granite. Jolly says it has no river sediments.

"That would suggest that it would contain any spill," he says.

"From a hydrogeological and a geomorphological point of view it's probably the better site."

Ancient flood history

Dr Mary Bourke, a geomorphologist with the Planetary Science Institute in Tucson in the US, has studied how central Australia's landforms have changed over the millennia.

While she has not worked specifically on the Harts Range, and declined to comment specifically on the site, she says the region generally has been subject to catastrophic rainfall and floods over time, and some rivers there have changed course.

"If you have rivers whose banks are composed of erodable materials, and generally we think in terms of gravels and sands, if the force of the river is high enough it can actually erode away that sediment."

She says periodic large floods have caused the Todd River, which at one point flows through Alice Springs, to change its course several times in the past 2000 years.

Bourke says the floods she is referring to are much larger than those in recorded history.

"Radioactive waste will be managed in a single, purpose-built, state of art facility, and as a result it will not present a hazard to either the community or the environment," DEST says.

"The hydrogeology and geomorphology of all potential sites will be examined during the site investigation studies," DEST says. "It is premature to offer further comment at this stage."

The two sites also host the Jindalee Facility Alice Springs, one of three operational radars the Australian government uses for surveillance of the country's northern coastline and beyond.

There are currently no plans to decommission the facility and the Department of Defence says an evaluation on the suitability of the sites is in its early phases and DEST will thoroughly investigate the impact on current radar operations and future research and development activities before making recommendations on the site.

DEST says there will be no impact on the continued operations of the Jindalee system.